rs3734397

Positions:

• chr6-10982615-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000354666.4(ELOVL2):​c.*1166C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,232 control chromosomes in the GnomAD database, including 54,450 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.84 (54444 hom., cov: 32)
  • Exomes 𝑓: 0.83 (6 hom.)
• Consequence: ELOVL2 ENST00000354666.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

Genes affected

ELOVL2 (HGNC:14416): (ELOVL fatty acid elongase 2) Enables fatty acid elongase activity. Involved in fatty acid elongation, polyunsaturated fatty acid and very long-chain fatty acid biosynthetic process. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELOVL2	NM_017770.4	c.*1166C>T		3_prime_UTR_variant	8/8	ENST00000354666.4	NP_060240.3
ELOVL2	XM_011514716.4	c.*1166C>T		3_prime_UTR_variant	8/8		XP_011513018.1
ELOVL2	XM_011514717.4	c.*1166C>T		3_prime_UTR_variant	8/8		XP_011513019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELOVL2	ENST00000354666.4	c.*1166C>T		3_prime_UTR_variant	8/8	1	NM_017770.4	ENSP00000346693	P1

Frequencies

GnomAD3 genomes AF: 0.841 AC: 127975 AN: 152096 Hom.: 54379 Cov.: 32

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.785

GnomAD4 exome AF: 0.833 AC: 15 AN: 18 Hom.: 6 Cov.: 0 AF XY: 0.786 AC XY: 11 AN XY: 14

Gnomad4 NFE exome AF: 0.833

GnomAD4 genome AF: 0.842 AC: 128101 AN: 152214 Hom.: 54444 Cov.: 32 AF XY: 0.846 AC XY: 62901 AN XY: 74388

Gnomad4 AFR AF: 0.961

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.936

Gnomad4 SAS AF: 0.876

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.786

Alfa AF: 0.780 Hom.: 53254

Bravo AF: 0.843

Asia WGS AF: 0.889 AC: 3088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.85

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3734397; hg19: chr6-10982848;